Spain's Contador jumped away from a group of top guns and built a small gap over his rivals some two kilometres from the finish of the 185-km ride from Carboneras de Guadazaon.
Winner Anacona of Colombia took the day's laurels after dropping his breakaway companions in the last climb, an 8-km ascent at an average gradient of 6.6 percent.
Giro d'Italia winner Quintana and Spain's Joaquim Rodriguez were the only riders who managed to catch Contador after the double Tour de France champion's brutal acceleration left his rivals stuck on the tar on an unusually wet day on the Vuelta.
Contador was a surprise starter last weekend in Jerez de la Frontera after fracturing his shinbone in the 10th stage of the Tour de France last month.
“It was a very good day for Alberto and I think everyone saw a very strong Contador in the finale," his Tinkoff-Saxo sports director said.
Quintana now leads Contador by three seconds overall with the Colombian's Movistar team mate Alejandro Valverde of Spain, who started the day in the red jersey, dropping to third eight seconds off the pace.
"I usually go well in all weather conditions but I was a little affected by the heat in the first days," said Quintana, who was second overall in last year's Tour de France.
"Today I had good legs and I worked to keep the jersey in the team."
Britain's Chris Froome, who also lost ground, is fifth, 28 seconds behind Quintana as Anacona moved up to fourth overall.
"In the finale I didn't have the legs to follow the top guys when they went," said Froome, who crashed out of the Tour de France on the fifth stage.
"But I think given where I've come from on the back of the Tour and the build-up into the race I'm really happy with how things have gone so far.
"I can definitely feel I'm starting to pick up that race rhythm back into my legs and I'm looking forward to the second half of this race."
Lampre-Merida rider Anacona dropped breakaway companions Bob Jungels of Luxembourg and Spain's Javi Moreno with 6.5 km left and never looked back.
Monday is a rest day and Tuesday's 10th stage is a 36.7-km individual time trial.
(Writing by Julien Pretot, editing by Ed Osmond)
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